ArticleMetabolites2020
JUMPm: A Tool for Large-Scale Identification of Metabolites in Untargeted Metabolomics.
Article in Metabolites, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Evaluation of MassFrontier, MetFrag, MS-FINDER, and SIRIUS for Metabolite Annotation Using an Experimental LC-HRMS Dataset.Biomedicines · 2026Article
- Targeting glycerophospholipid biosynthesis overcomes chemoresistance driven by SLFN11 loss in Ewing sarcoma.Cell death & disease · 2026Article
- Extracellular Vesicles From Chylomicron-Treated Endothelial Cells Drive Macrophage Inflammation.Arteriosclerosis, thrombosis, and vascular biology · 2025Article
- Article
- STK11 coordinates IL-4 signaling with metabolic reprogramming to control M2 macrophage polarization and antitumor immunity.Science advances · 2025Article
- Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in post-transcriptional repression of starvation-induced pathways.bioRxiv : the preprint server for biology · 2025Article
- Microbial contribution to metabolic niche formation varies across the respiratory tract.Cell host & microbe · 2025Article
- The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency.Microbiome · 2025Article
- JUMPlib: Integrative Search Tool Combining Fragment Ion Indexing with Comprehensive TMT Spectral Libraries.Journal of proteome research · 2025Article
- CYP3A5 unexpectedly regulates glucose metabolism through the AKT-TXNIP-GLUT1 axis in pancreatic cancer.Genes & diseases · 2024Article
- Profiling Mouse Brain Single-Cell-Type Proteomes Via Adeno-Associated Virus-Mediated Proximity Labeling and Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Article
- Prospects and challenges of cancer systems medicine: from genes to disease networks.Briefings in bioinformatics · 2022Review
- Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification.Nature methods · 2021Article
Corrections and comments
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Authors and funding
9 authors.
Funding
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Abstract
Metabolomics is increasingly important for biomedical research, but large-scale metabolite identification in untargeted metabolomics is still challenging. Here, we present Jumbo Mass spectrometry-based Program of Metabolomics (JUMPm) software, a streamlined software tool for identifying potential metabolite formulas and structures in mass spectrometry. During database search, the false discovery rate is evaluated by a target-decoy strategy, where the decoys are produced by breaking the octet rule of chemistry. We illustrated the utility of JUMPm by detecting metabolite formulas and structures from liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) analyses of unlabeled and stable-isotope labeled yeast samples. We also benchmarked the performance of JUMPm by analyzing a mixed sample from a commercially available metabolite library in both hydrophilic and hydrophobic LC-MS/MS. These analyses confirm that metabolite identification can be significantly improved by estimating the element composition in formulas using stable isotope labeling, or by introducing LC retention time during a spectral library search, which are incorporated into JUMPm functions. Finally, we compared the performance of JUMPm and two commonly used programs, Compound Discoverer 3.1 and MZmine 2, with respect to putative metabolite identifications. Our results indicate that JUMPm is an effective tool for metabolite identification of both unlabeled and labeled data in untargeted metabolomics.
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